August 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 326477: implement influxdb error reporter
by GitHub 31 Aug '17

31 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 326477d957bda9c32f63497b5fc911e8c2a9731d https://github.com/galaxyproject/galaxy/commit/326477d957bda9c32f63497b5fc9… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M config/error_report.yml.sample M doc/source/admin/special_topics/bug_reports.rst A lib/galaxy/tools/error_reports/plugins/influxdb.py Log Message: ----------- implement influxdb error reporter Commit: f67fa22dd9bd05d72df859065a3e126af0161d62 https://github.com/galaxyproject/galaxy/commit/f67fa22dd9bd05d72df859065a3e… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M lib/galaxy/tools/error_reports/plugins/influxdb.py M lib/galaxy/tools/error_reports/plugins/json.py M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- also add destination id everywhere Commit: 7db1a3fb3e6f61540f1354a899fce1c55e834775 https://github.com/galaxyproject/galaxy/commit/7db1a3fb3e6f61540f1354a899fc… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M config/error_report.yml.sample M doc/source/admin/special_topics/bug_reports.rst A lib/galaxy/tools/error_reports/plugins/influxdb.py M lib/galaxy/tools/error_reports/plugins/json.py M lib/galaxy/tools/error_reports/plugins/sentry.py Log Message: ----------- Merge pull request #4533 from erasche/influxdb-error-reporter Implement influxdb error reporter Compare: https://github.com/galaxyproject/galaxy/compare/49f243862207...7db1a3fb3e6f

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[galaxyproject/galaxy] b75f79: Load tools with collection type source attributes ...
by GitHub 31 Aug '17

31 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b75f793ea4c58786747da3a9571ba3bd938cd181 https://github.com/galaxyproject/galaxy/commit/b75f793ea4c58786747da3a9571b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Load tools with collection type source attributes into the workflow editor. Should allow using filter failed and merge collection tools within workflows. Commit: ba8a7f0e3a540c99b3d8e7be3ea67008e2e76ff2 https://github.com/galaxyproject/galaxy/commit/ba8a7f0e3a540c99b3d8e7be3ea6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/mvc/workflow/workflow-view-terminals.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view-terminals.js Log Message: ----------- Pack client. Commit: 01d16358efa5a71f7030c48c302129cca515e6c6 https://github.com/galaxyproject/galaxy/commit/01d16358efa5a71f7030c48c3021… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M static/maps/mvc/workflow/workflow-terminals.js.map Log Message: ----------- Adjust JS styling for workflow-terminal.js. Commit: 49f2438622075f3e9cbe9097ad31b177c97f532a https://github.com/galaxyproject/galaxy/commit/49f2438622075f3e9cbe9097ad31… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py M static/maps/mvc/workflow/workflow-terminals.js.map M static/maps/mvc/workflow/workflow-view-terminals.js.map M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/workflow/workflow-terminals.js M static/scripts/mvc/workflow/workflow-view-terminals.js Log Message: ----------- Merge pull request #4514 from jmchilton/collection_operations Load tools with collection type source attributes into the workflow editor Compare: https://github.com/galaxyproject/galaxy/compare/d09ced249d72...49f243862207

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[galaxyproject/galaxy] 43fd81: More logging for selenium tests.
by GitHub 31 Aug '17

31 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 43fd81df59c1862c745813e3b340e93976ef1e2b https://github.com/galaxyproject/galaxy/commit/43fd81df59c1862c745813e3b340… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M test/galaxy_selenium/driver_factory.py M test/selenium_tests/framework.py Log Message: ----------- More logging for selenium tests. Dumb the browser log and the driver log out as JSON to the test error directory for that test. Commit: f35fed29356d1f55af803f2f24cd2e54634cc8a6 https://github.com/galaxyproject/galaxy/commit/f35fed29356d1f55af803f2f24cd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M test/galaxy_selenium/sizzle.py A test/selenium_tests/test_sizzle_loading.py Log Message: ----------- Improve setting up Sizzle for Selenium tests. Something releated to AMD broke our way of injecting Sizzle into Galaxy for Selenium tests. This is a much better way that seems to work - just use jQuery ($) as Sizzle if it is available. Avoids an external dependency and another page fetch per test as well as fixing the problem. Add a test case that just tests the sizzle stuff works on its own. It will be a clear indiciation what is broken if there are related regressions in the future. Commit: d09ced249d729b5c0a2098a9d5e81472c91f62b6 https://github.com/galaxyproject/galaxy/commit/d09ced249d729b5c0a2098a9d5e8… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M test/galaxy_selenium/driver_factory.py M test/galaxy_selenium/sizzle.py M test/selenium_tests/framework.py A test/selenium_tests/test_sizzle_loading.py Log Message: ----------- Merge pull request #4523 from jmchilton/selenium_fixes_15 Selenium test fixes and improvements. Compare: https://github.com/galaxyproject/galaxy/compare/823eb1d4ec84...d09ced249d72

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[galaxyproject/usegalaxy-playbook] c2a31c: Implicit FTPS for Main
by GitHub 31 Aug '17

31 Aug '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c2a31c974a32b624d67e9508a2d20b0a6bfd7600 https://github.com/galaxyproject/usegalaxy-playbook/commit/c2a31c974a32b624… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M env/main/group_vars/ftpservers/vars.yml Log Message: ----------- Implicit FTPS for Main Commit: e182b92886f820027e54ba7b1ae96793475cda80 https://github.com/galaxyproject/usegalaxy-playbook/commit/e182b92886f82002… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M env/test/group_vars/ftpservers/vars.yml Log Message: ----------- Correction for a harmless ProFTPD config error Commit: d9fae1cdf31102f33b981eeb2d9a6a1f6cfc8d2a https://github.com/galaxyproject/usegalaxy-playbook/commit/d9fae1cdf31102f3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M roles/usegalaxy_privileged/templates/archive_logs.sh.j2 Log Message: ----------- Fix Galaxy log rotation Commit: 0a5fe4b442509159560a15f555f1a5eafe33cd6e https://github.com/galaxyproject/usegalaxy-playbook/commit/0a5fe4b442509159… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_data_manager_conf.xml M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Updated mutable configs Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/d4ea9ac0c217...…

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[galaxyproject/galaxy] 514250: Make a couple workflow invocation tests more robus...
by GitHub 31 Aug '17

31 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5142509f131591b978ecadebbaefc1bb6f608f47 https://github.com/galaxyproject/galaxy/commit/5142509f131591b978ecadebbaef… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M test/api/test_workflows.py Log Message: ----------- Make a couple workflow invocation tests more robust. Less random sleeping, wait for actual invocation. I think this is likely the cause this transient failure (https://jenkins.galaxyproject.org/job/docker-api/8215/testReport/junit/api.…) picking up the input as the last dataset in the history instead of the output - I bet the workflow just hadn't been invoked yet. Commit: 823eb1d4ec84f17f92e4bbf2a12194b2bc0ea9d0 https://github.com/galaxyproject/galaxy/commit/823eb1d4ec84f17f92e4bbf2a121… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-31 (Thu, 31 Aug 2017) Changed paths: M test/api/test_workflows.py Log Message: ----------- Merge pull request #4530 from jmchilton/api_test_fixes More robust workflow invocation testing. Compare: https://github.com/galaxyproject/galaxy/compare/bd13cadbddbb...823eb1d4ec84

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[galaxyproject/galaxy] e8de89: Display d3 hierarchy files in uploader
by GitHub 30 Aug '17

30 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e8de89afd56b5e125e1e879855d7168a7d2c79b5 https://github.com/galaxyproject/galaxy/commit/e8de89afd56b5e125e1e879855d7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Display d3 hierarchy files in uploader Commit: bd13cadbddbbd991460095ad94d9c974cc2a40c9 https://github.com/galaxyproject/galaxy/commit/bd13cadbddbbd991460095ad94d9… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #4522 from guerler/d3_hierarchy_in_uploader Display d3 hierarchy datatype in upload interface Compare: https://github.com/galaxyproject/galaxy/compare/2f9cd0ee491c...bd13cadbddbb

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[galaxyproject/galaxy] 5ab286: Prevent transient job state test failures from fai...
by GitHub 30 Aug '17

30 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5ab28634cabc1df2aa14e9db303247e41b9ea311 https://github.com/galaxyproject/galaxy/commit/5ab28634cabc1df2aa14e9db3032… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M test/api/test_jobs.py Log Message: ----------- Prevent transient job state test failures from failing the build. A precondition to the real meat of the test is failing to be met sometimes in production - this failure is indicating a problem with the test and not with Galaxy. I previously tried to address this with https://github.com/galaxyproject/galaxy/pull/3988 but that didn't work. Now if the trainsient ok occurs the test will be skipped. Most of the time it won't skip and the rest of the test will execute and ensure there aren't regressions in behaviors related to cleaning up datasets after job completion. I'm placing the skips a couple different places so hopefully we can get a stack trace at somepoint - knowing where the code is when the job state is changing from running to ok will help puzzle out what is handing for the two minutes the job is running in the test framework. Commit: 2f9cd0ee491cc99af4a64416e21ce95e6e7dbb33 https://github.com/galaxyproject/galaxy/commit/2f9cd0ee491cc99af4a64416e21c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M test/api/test_jobs.py Log Message: ----------- Merge pull request #4510 from jmchilton/job_test_fix Prevent transient job state test failures from failing the build. Compare: https://github.com/galaxyproject/galaxy/compare/f3b8a121b7d9...2f9cd0ee491c

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[galaxyproject/galaxy] eefc26: add the first test: history grid
by GitHub 30 Aug '17

30 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: eefc268eae2961186a84dc396921326549ea4822 https://github.com/galaxyproject/galaxy/commit/eefc268eae2961186a84dc396921… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-08-23 (Wed, 23 Aug 2017) Changed paths: A test/selenium_tests/test_published_history_grid.py Log Message: ----------- add the first test: history grid Commit: b664f26aa0d7a3ad151f236ba569efecb09a5526 https://github.com/galaxyproject/galaxy/commit/b664f26aa0d7a3ad151f236ba569… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-08-23 (Wed, 23 Aug 2017) Changed paths: M test/selenium_tests/test_published_history_grid.py Log Message: ----------- add standard search test Commit: 0e1cbc09f8a604c1b45127faf30170ba1b67bb1b https://github.com/galaxyproject/galaxy/commit/0e1cbc09f8a604c1b45127faf301… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-08-23 (Wed, 23 Aug 2017) Changed paths: M test/selenium_tests/test_published_history_grid.py Log Message: ----------- add 'sort by name/owner' tests Commit: 72195e14baa5e5f3131f2364858e71c4e4fb960c https://github.com/galaxyproject/galaxy/commit/72195e14baa5e5f3131f2364858e… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-08-25 (Fri, 25 Aug 2017) Changed paths: M test/selenium_tests/test_published_history_grid.py Log Message: ----------- [WIP]: add advanced search tests Commit: 2403916c7b6a29810e74cb3485d3634ef904dde6 https://github.com/galaxyproject/galaxy/commit/2403916c7b6a29810e74cb3485d3… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-08-26 (Sat, 26 Aug 2017) Changed paths: M test/selenium_tests/test_published_history_grid.py Log Message: ----------- test clicking tags Commit: 2f547b09737d6711e44de7d9c7600384aa97038e https://github.com/galaxyproject/galaxy/commit/2f547b09737d6711e44de7d9c760… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-08-26 (Sat, 26 Aug 2017) Changed paths: M test/selenium_tests/test_published_history_grid.py Log Message: ----------- small improvements Commit: da1518db48265617cb2e2a00f9b738058c648f4b https://github.com/galaxyproject/galaxy/commit/da1518db48265617cb2e2a00f9b7… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-08-26 (Sat, 26 Aug 2017) Changed paths: M test/selenium_tests/test_published_history_grid.py Log Message: ----------- set annotations Commit: 2dda34a00240a9af990a23c14cd73abb87db4268 https://github.com/galaxyproject/galaxy/commit/2dda34a00240a9af990a23c14cd7… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-08-26 (Sat, 26 Aug 2017) Changed paths: A test/selenium_tests/test_published_histories_grid.py R test/selenium_tests/test_published_history_grid.py Log Message: ----------- rename the file Commit: 773029bd364037943a810506a79cebca85f2a260 https://github.com/galaxyproject/galaxy/commit/773029bd364037943a810506a79c… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2017-08-28 (Mon, 28 Aug 2017) Changed paths: M test/selenium_tests/test_published_histories_grid.py Log Message: ----------- fix flake8 issues Commit: a464fe9db6ab993e282feb1ba9ec4eea78ada376 https://github.com/galaxyproject/galaxy/commit/a464fe9db6ab993e282feb1ba9ec… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M test/selenium_tests/test_published_histories_grid.py Log Message: ----------- Rework published histories selenium test a bit. - Wait for elements to be clickable before clicking them. - Allow individual tests to be run on their own and out of order. - Use randomly generated emails - the tests still can't really be applied to an external Galaxy test server but this gets us closer. Commit: f3b8a121b7d9d5535381aa8cae7887bd978f9678 https://github.com/galaxyproject/galaxy/commit/f3b8a121b7d9d5535381aa8cae78… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: A test/selenium_tests/test_published_histories_grid.py Log Message: ----------- Merge pull request #4502 from anatskiy/published_history_test Published History Grid tests Compare: https://github.com/galaxyproject/galaxy/compare/21eac0d445cb...f3b8a121b7d9

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[galaxyproject/galaxy] 2d9ae7: Fix another bad merge issue?
by GitHub 30 Aug '17

30 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2d9ae75cae83969b3a708c0921ca33841ad08ef5 https://github.com/galaxyproject/galaxy/commit/2d9ae75cae83969b3a708c0921ca… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Fix another bad merge issue? Commit: 21eac0d445cbf8523cd48402d0992dc7ff1720c6 https://github.com/galaxyproject/galaxy/commit/21eac0d445cbf8523cd48402d099… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Merge pull request #4515 from jmchilton/another_merge_issue Fix subdirectory listing for extra files Compare: https://github.com/galaxyproject/galaxy/compare/d56fcf6777d9...21eac0d445cb

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[galaxyproject/usegalaxy-playbook] c565b0: Upgrade galaxyproject.proftpd
by GitHub 29 Aug '17

29 Aug '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c565b0e7b893ee4a455cc6889e5c9d6578422c0d https://github.com/galaxyproject/usegalaxy-playbook/commit/c565b0e7b893ee4a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M roles/galaxyproject.proftpd/README.md M roles/galaxyproject.proftpd/defaults/main.yml M roles/galaxyproject.proftpd/handlers/main.yml A roles/galaxyproject.proftpd/meta/.galaxy_install_info M roles/galaxyproject.proftpd/tasks/debian.yml M roles/galaxyproject.proftpd/tasks/galaxy_auth.yml M roles/galaxyproject.proftpd/tasks/main.yml M roles/galaxyproject.proftpd/tasks/redhat.yml M roles/galaxyproject.proftpd/tasks/tls.yml M roles/galaxyproject.proftpd/templates/galaxy_auth.conf.j2 A roles/galaxyproject.proftpd/templates/global.conf.j2 M roles/galaxyproject.proftpd/templates/tls.conf.j2 A roles/galaxyproject.proftpd/templates/virtualhost.conf.j2 M roles/galaxyproject.proftpd/tests/test.yml M roles/galaxyproject.proftpd/vars/main.yml Log Message: ----------- Upgrade galaxyproject.proftpd Commit: d4ea9ac0c2171835d9228955d68a84777040c19b https://github.com/galaxyproject/usegalaxy-playbook/commit/d4ea9ac0c2171835… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-29 (Tue, 29 Aug 2017) Changed paths: M env/common/stack.yml M env/test/group_vars/dbservers/vault.yml R env/test/group_vars/ftpservers.yml A env/test/group_vars/ftpservers/vars.yml A env/test/group_vars/ftpservers/vault.yml Log Message: ----------- Enable implicit FTPS on Test Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/234608edacbe...…

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